Jim Procter [Tue, 22 Aug 2017 10:37:03 +0000 (11:37 +0100)]
JAL-1950 patch after merge
Jim Procter [Mon, 21 Aug 2017 18:57:44 +0000 (19:57 +0100)]
Merge branch 'develop' into trial_merge/JAL-1950
Conflicts:
src/jalview/gui/RestServiceEditorPane.java
src/jalview/schemes/AnnotationColourGradient.java
src/jalview/ws/rest/RestClient.java
src/jalview/ws/rest/RestJobThread.java
Shmmr client definition refactored.
AnnotationColourGradient includes 'fade to grey' P-value+E-value shading
Jim Procter [Mon, 21 Aug 2017 13:47:51 +0000 (14:47 +0100)]
Merge branch 'documentation/JAL-2675_release2102b1' into develop
Jim Procter [Mon, 21 Aug 2017 13:46:45 +0000 (14:46 +0100)]
JAL-2675 typo in what's new href
gmungoc [Mon, 21 Aug 2017 13:06:46 +0000 (14:06 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Conflicts:
src/MCview/PDBChain.java
src/jalview/analysis/AlignmentSorter.java
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/Dna.java
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/appletgui/Finder.java
src/jalview/appletgui/SeqPanel.java
src/jalview/commands/EditCommand.java
src/jalview/datamodel/AlignedCodonFrame.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/Finder.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/SeqCanvas.java
src/jalview/gui/SeqPanel.java
src/jalview/io/FeaturesFile.java
src/jalview/io/JSONFile.java
src/jalview/io/gff/InterProScanHelper.java
src/jalview/io/vamsas/Datasetsequence.java
src/jalview/renderer/seqfeatures/FeatureRenderer.java
src/jalview/util/RangeComparator.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
src/jalview/ws/jws2/AADisorderClient.java
Jim Procter [Fri, 18 Aug 2017 13:15:40 +0000 (14:15 +0100)]
JAL-2675 bump version for branch to 2.10.2b1
Jim Procter [Fri, 18 Aug 2017 13:13:28 +0000 (14:13 +0100)]
JAL-1551 formatting
Jim Procter [Fri, 18 Aug 2017 13:08:03 +0000 (14:08 +0100)]
JAL-2675 release notes entry for 2.10.2b1, updated what’s new and link to latest notes in help.
Jim Procter [Thu, 17 Aug 2017 12:07:53 +0000 (13:07 +0100)]
JAL-2418 ahem - correct year for what's new
Jim Procter [Thu, 17 Aug 2017 11:37:50 +0000 (12:37 +0100)]
JAL-2418 JAL-2116 use single j2se 7+ argumant with java 9 add-modules - seems to work on java 8 (windows, osx, linux) without 'use latest version' popup and also on java 9
Jim Procter [Thu, 17 Aug 2017 10:41:33 +0000 (11:41 +0100)]
JAL-2418 JAL-2116 make sure java 8,7 vm args are also listed
Jim Procter [Wed, 16 Aug 2017 22:24:25 +0000 (23:24 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 22:24:13 +0000 (23:24 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 22:23:59 +0000 (23:23 +0100)]
JAL-2418 formatting
Jim Procter [Wed, 16 Aug 2017 22:23:53 +0000 (23:23 +0100)]
JAL-2418 occupancy row in What’s New
Jim Procter [Wed, 16 Aug 2017 21:37:37 +0000 (22:37 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 21:30:21 +0000 (22:30 +0100)]
JAL-2418 add GPL to main sources
Jim Procter [Wed, 16 Aug 2017 21:22:11 +0000 (22:22 +0100)]
JAL-2418 source formatting
Jim Procter [Wed, 16 Aug 2017 20:52:55 +0000 (21:52 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 16 Aug 2017 20:52:36 +0000 (21:52 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 20:52:07 +0000 (21:52 +0100)]
JAL-2418 mirror fonts option doc tweak
Jim Procter [Wed, 16 Aug 2017 19:17:43 +0000 (20:17 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 16 Aug 2017 19:17:03 +0000 (20:17 +0100)]
JAL-2418 whats new for 2.10.2
Jim Procter [Wed, 16 Aug 2017 19:16:52 +0000 (20:16 +0100)]
JAL-2418 reclassify some issues to features/bugs resolved
Jim Procter [Wed, 16 Aug 2017 18:23:33 +0000 (19:23 +0100)]
JAL-2418 typos in release notes
Jim Procter [Wed, 16 Aug 2017 18:16:08 +0000 (19:16 +0100)]
JAL-2418 check groovy script one-liners for restoring legacy score model behaviour
Jim Procter [Tue, 15 Aug 2017 16:15:25 +0000 (17:15 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Tue, 15 Aug 2017 16:14:32 +0000 (17:14 +0100)]
JAL-2116 fix typo in build.xml for j2se element
Jim Procter [Tue, 15 Aug 2017 15:55:22 +0000 (16:55 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Tue, 15 Aug 2017 15:55:06 +0000 (16:55 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 15 Aug 2017 14:02:19 +0000 (15:02 +0100)]
JAL-2418 bump release to Thursday
Jim Procter [Tue, 15 Aug 2017 13:54:20 +0000 (14:54 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Mon, 14 Aug 2017 16:25:16 +0000 (17:25 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 16:23:46 +0000 (17:23 +0100)]
JAL-2418 release notes for JAL-2663
Jim Procter [Mon, 14 Aug 2017 16:21:45 +0000 (17:21 +0100)]
Merge branch 'patch/JAL-2335_filterAACons' into develop
Jim Procter [Mon, 14 Aug 2017 16:21:16 +0000 (17:21 +0100)]
Merge branch 'patch/JAL-2116_java9' into develop
Jim Procter [Mon, 14 Aug 2017 16:20:28 +0000 (17:20 +0100)]
JAL-2116 add 1.8 1.7 compatible launch string
Jim Procter [Mon, 14 Aug 2017 13:17:35 +0000 (14:17 +0100)]
JAL-2335 choose appropriate alphabet for filtering nonstandard symbols
Jim Procter [Mon, 14 Aug 2017 13:16:27 +0000 (14:16 +0100)]
JAL-2335 source formatting
Jim Procter [Mon, 14 Aug 2017 13:16:17 +0000 (14:16 +0100)]
JAL-2335 filterNonStandardResidues configurable for jabaws clients
Jim Procter [Mon, 14 Aug 2017 09:45:14 +0000 (10:45 +0100)]
Merge branch 'patch/JAL-2116_java9' into develop
Jim Procter [Mon, 14 Aug 2017 09:45:05 +0000 (10:45 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 09:44:25 +0000 (10:44 +0100)]
JAL-2116 switch to java.se.ee https://bugs.openjdk.java.net/browse/JDK-8166438
Jim Procter [Mon, 14 Aug 2017 09:35:00 +0000 (10:35 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 14 Aug 2017 09:34:44 +0000 (10:34 +0100)]
Merge branch 'patch/JAL-2663_filterAACons' into develop
Jim Procter [Mon, 14 Aug 2017 09:33:33 +0000 (10:33 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Sun, 13 Aug 2017 14:34:58 +0000 (15:34 +0100)]
JAL-2663 flag and filter to exclude non-standard amino acids from submission
Jim Procter [Sun, 13 Aug 2017 14:34:20 +0000 (15:34 +0100)]
JAL-2663 source formatting
Jim Procter [Thu, 10 Aug 2017 20:11:21 +0000 (21:11 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 20:10:23 +0000 (21:10 +0100)]
JAL-2116 try '=' syntax jigsaw-dev.1059479.n5.nabble.com/Java-9-EA-169-Webstart-NoClassDefFoundError-javax-xml-ws-Service-td5716769.html
Jim Procter [Thu, 10 Aug 2017 19:42:30 +0000 (20:42 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 19:38:36 +0000 (20:38 +0100)]
JAL-2116 test java 9 only JNLP launch
Jim Procter [Thu, 10 Aug 2017 15:38:21 +0000 (16:38 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 15:37:30 +0000 (16:37 +0100)]
JAL-2116 explicit replace j2se element with a java9 specific one since orangevolt-tasks don't support the java-vm-args attribute
gmungoc [Thu, 10 Aug 2017 15:24:53 +0000 (16:24 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Jim Procter [Thu, 10 Aug 2017 14:38:30 +0000 (15:38 +0100)]
Merge branch 'patch/JAL-2116_java9' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 14:37:16 +0000 (15:37 +0100)]
JAL-2116 java9 modules dependency for JNLP file
gmungoc [Thu, 10 Aug 2017 11:56:12 +0000 (12:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 10 Aug 2017 11:29:52 +0000 (12:29 +0100)]
JAL-2660 used saved value of ignoreGapsInConsensus when loading
(/copying) viewport
Jim Procter [Thu, 10 Aug 2017 09:31:54 +0000 (10:31 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Thu, 10 Aug 2017 09:31:39 +0000 (10:31 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Thu, 10 Aug 2017 09:31:23 +0000 (10:31 +0100)]
JAL-2418 set final release date to 15th August 2017 for 2.10.2
Signed-off-by: Jim Procter <jprocter@issues.jalview.org>
Jim Procter [Thu, 10 Aug 2017 09:30:00 +0000 (10:30 +0100)]
JAL-2418 typo in release notes
Jim Procter [Thu, 10 Aug 2017 09:29:53 +0000 (10:29 +0100)]
JAL-2418 known defect for JAL-2321 in release notes
Jim Procter [Thu, 10 Aug 2017 09:19:29 +0000 (10:19 +0100)]
JAL-2418 reorganised release notes to topic sections rather than General/Application/Applet
gmungoc [Thu, 10 Aug 2017 09:17:14 +0000 (10:17 +0100)]
JAL-2505 apply changed description to new, not deleted, feature!
gmungoc [Thu, 10 Aug 2017 09:10:51 +0000 (10:10 +0100)]
JAL-2658 ensure features dropdown entries are unique
gmungoc [Thu, 10 Aug 2017 07:52:56 +0000 (08:52 +0100)]
JAL-2593 don't filter out 'colour by label' features
gmungoc [Thu, 10 Aug 2017 07:12:06 +0000 (08:12 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
Jim Procter [Wed, 9 Aug 2017 20:40:35 +0000 (21:40 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 9 Aug 2017 20:40:25 +0000 (21:40 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 9 Aug 2017 20:40:05 +0000 (21:40 +0100)]
JAL-2418 JAL-2398 JAL-2397 simpler documentation for reinstating legacy behaviour
Jim Procter [Wed, 9 Aug 2017 20:15:55 +0000 (21:15 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Wed, 9 Aug 2017 20:15:27 +0000 (21:15 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 9 Aug 2017 20:14:58 +0000 (21:14 +0100)]
JAL-2397 JAL-2398 documentation for reinstating legacy PCA calculation with asymmetric Blosum62 matrix.
Jim Procter [Wed, 9 Aug 2017 19:24:00 +0000 (20:24 +0100)]
JAL-2426 Rfam download suffix
Jim Procter [Wed, 9 Aug 2017 18:32:05 +0000 (19:32 +0100)]
JAL-2426 JAL-1270 report Xfam download URL used if debug enabled
Jim Procter [Wed, 9 Aug 2017 18:31:29 +0000 (19:31 +0100)]
JAL-2425 raw stockholm download URLs
Jim Procter [Wed, 9 Aug 2017 18:29:54 +0000 (19:29 +0100)]
JAL-1270 testProps should also enable debug logging
Jim Procter [Wed, 9 Aug 2017 18:29:05 +0000 (19:29 +0100)]
JAL-2425 test for alignment metadata retrieved from Pfam and Rfam
Jim Procter [Wed, 9 Aug 2017 18:27:53 +0000 (19:27 +0100)]
JAL-2425 remove overloaded getSequenceRecords method (don’t need it ?)
Jim Procter [Wed, 9 Aug 2017 15:44:02 +0000 (16:44 +0100)]
JAL-2418 release notes
gmungoc [Wed, 9 Aug 2017 10:45:53 +0000 (11:45 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Wed, 9 Aug 2017 09:28:58 +0000 (10:28 +0100)]
JAL-2480 inline one method, improve comments
Jim Procter [Wed, 9 Aug 2017 08:46:08 +0000 (09:46 +0100)]
JAL-2418 more release notes
Jim Procter [Wed, 9 Aug 2017 08:45:50 +0000 (09:45 +0100)]
JAL-2418 JAL-2611 and rejigged overview documentation
Jim Procter [Wed, 9 Aug 2017 08:09:56 +0000 (09:09 +0100)]
Merge branch 'bug/JAL-2634' into develop
Jim Procter [Wed, 9 Aug 2017 07:56:01 +0000 (08:56 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
gmungoc [Wed, 9 Aug 2017 07:39:23 +0000 (08:39 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Tue, 8 Aug 2017 15:44:45 +0000 (16:44 +0100)]
JAL-2560 alternative fix (reinstate lost line of code)
gmungoc [Tue, 8 Aug 2017 10:30:04 +0000 (11:30 +0100)]
Merge branch 'develop' into features/JAL-2446NCList
gmungoc [Tue, 8 Aug 2017 10:18:12 +0000 (11:18 +0100)]
JAL-2649 JAL-2650 wait for Conservation calc to complete before setting
on new View coloured by Conservation
gmungoc [Tue, 8 Aug 2017 09:08:46 +0000 (11:08 +0200)]
JAL-2650 configure new viewport settings before selecting view tab
Jim Procter [Mon, 7 Aug 2017 14:33:47 +0000 (15:33 +0100)]
Merge branch 'bug/JAL-2592userDefinedScheme' into develop
gmungoc [Mon, 7 Aug 2017 14:09:57 +0000 (16:09 +0200)]
Merge branch 'develop' into features/JAL-2446NCList
Jim Procter [Mon, 7 Aug 2017 13:31:35 +0000 (14:31 +0100)]
Merge branch 'develop' into releases/Release_2_10_2_Branch
Jim Procter [Mon, 7 Aug 2017 13:31:13 +0000 (14:31 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 7 Aug 2017 11:24:05 +0000 (12:24 +0100)]
JAL-2418 JAL-2468 known issue
Jim Procter [Mon, 7 Aug 2017 11:07:45 +0000 (12:07 +0100)]
JAL-2482 JAL-2487 documented in release notes
Jim Procter [Mon, 7 Aug 2017 11:04:48 +0000 (12:04 +0100)]
JAL-2482 release notes
git://source.jalview.org / jalview.git / log